go with the clone motor. flatheads are being phased out as some of the parts are not being produced anymore (actually for a couple years now) the shortage is in pistons specifically the chrome pistons that are needed for the cool bore (aluminum cylinder) you are looking at at least $100 to have a flatehead sleaved. also a good clone with the same mods as a flathead will make more power than a good blueprinted race ready flathead. you can make a 10hp clone for close to $500 including a clutch! try to do that with a flathead. here is a picture of my flathead on my race kart....
here is the inside of the carb...
now your talking a full out race motor here, this is what they call a controlled stock. it cost probably around $750 with labor and parts and still only makes between 10-15 hp. here are some specs...
bored carb to .715 with thin custom butteryfly and lots of custom tricks $200+
billet rod with r3 .030 over CHROME PISTON $50+ if you can find one
angle decked block and head cut for valve lift (no one cuts the eyebrows that much anymore) $100+
fully ported and polished $50+
header&muffler $75
stock flywheel
billet lifters and dyno cams cs4 cam 265 lift $80
dual valve springs $30
pvc valve setup $25
this motor also runs on alcohol ($5 per gallon) and will turn 8500 rpms plus!
your talking alot of money and this a race motor built to wka rules.
you can do this on gas in a clone and still have money left over to get a tav unit.
if you still decided to build a flathead let me know, i have lots of parts.
oh here is were karting is headed.... briggs animal... $1250
http://www.jcspecialty.net/img/pages/2.jpg